By Gabriel Yahya Haage, Raina Fan, Francis Van Oordt, Maria Creighton
As part of the Field Course, students took a trip to the STRI institution on Barro Colorado Island (BCI). Here we met with scientists and participated in student projects. While one group, henceforth known as the “uncool” group, was involved in some weevil collection madness, our project led us on a night hike on the island, where we collected katydids, which, as we all know, are way cooler than weevils. But katydids were not our only targets. We also caught geckos and frogs so that we could swab the inside of their mouths and their bodies. And why did we do this? To get a hold of their sweet, sweet micro-biomes, of course. We then used data (sadly not the samples we collected, due to time constraints), to try to understand differences in the micro-biomes of 7 amphibian species. Below are the highlights by each member of our group. They may be scientific or not, but all these events were a part of our Barro Colorado experience.
For me, visiting the Katydid Lab was the highpoint of the project. Getting to hold different katydids, many bearing wild coloration and each with its own personality (to the extent that an insect can have a personality) was a great experience. The way that the katydid researchers spoke to us clearly revealed their passion for their work that I left the lab seriously considering getting a katydid as a pet.
Trapping katydids was also easier than the other organisms we went out to get during the night hike. For one, they were more abundant. For another, once the Ziplock bag was placed on them, they tended to jump up, giving us the opportunity to close the bag, making sure to leave some air for them. Geckos and frogs were trickier. Geckos had the unfair advantage of walking on walls, so catching them required lunging at the wall while jumping upwards in order to lay our hands on them. Since we wanted to swab for their micro-biomes, everything had to be as sterile as possible, which meant wearing gloves and washing the skin of the specimen before we could swab them. The gloves can also help when the geckos choose to bite. If you’re lucky, it’ll sink its teeth into the glove and not your fingers (I was not so lucky…). In the end, whether katydids or geckos or frogs, this night expedition in Barro Colorado Island will be hard to forget.
Our collections night was definitely a highlight for me. We waited until a few hours after sundown before strapping on our headlamps and heading out with an “anything goes” attitude.
I was at first skeptical about whether we would be able to actually catch anything that we found — I would describe myself as the opposite of agile — but turns out there are some secret techniques™ to catching and swabbing small animals. I’ve compiled a few things I learned about how to be a real-life Pokemon master:
1. Let there be light
Like most humans, I see worse at night. In fact, I barely notice cryptic small animals during the day. Unsurprisingly, this can be a problem when your study species are nocturnal. Luckily, we learned that many of our insect, reptilian and amphibian target species tend to congregate around light sources at night. I don’t think there’s consensus yet in the scientific community as to why this is the case, but some theories suggest that artificial lights interfere with insects’ ability to navigate through phototaxis (navigating by moving relative to a light source, such as the moon. Other theories include artificial light containing frequencies similar to that of female moth pheromones, so male moths are responding to what they perceive as a mating signal. Whatever the reason, light sources are a great place to look for moths, katydids, dragonflies and more during the night. And where you find insects, you might also find animals that enjoy snacking on them, such as geckos, frogs and lizards.
There exists a lot literature detailing the use of light traps to catch insect specimens. For our adventure, we were fortunate to be able to explore the multitude of well-lit STRI research buildings adjacent to the rich tropical forest of BCI. We got hits very early on and ended up seeing quite a few cool species, including various beetles, dragonflies, geckos, and even freshly-laid frog eggs. Turns out, finding bugs and reptiles can be easy — catching them is another story
2. Yes you (garbage) can
There are two parts to this one: first, get creative with your resources. Second, confidence.
Sure, wall-scaling geckos are pretty fast. But you’re human; you have the largest encephalization quotient (brain-to-body mass ratio) of the animal kingdom. Humans needn’t be the fastest or the strongest when they have ingenuity. So when you see a gecko three feet above your head zipping around at the speed of light, don’t fret — use that unusually large prefrontal cortex and come up with a plan.
Our ingenious plan involved locating a nearby empty garbage bin, flipping it over, and getting a tall person (me) to stand precariously on top of it with an outstretched arm. To my utter amazement, it actually worked! It does help to keep a light shined on your target to freeze it in place while you slowly creep your hand towards it. Finish by snatching it in one swift motion. This is where confidence is key — commit to the capture and don’t waver.
I should note that you should take precautions to make sure you don’t hurt your specimen in the process. For reptiles, it’s best to grab them in a manner where they can’t struggle too much or eject their tail (see above). For insects, you’ll often have better luck trapping them with a bag rather than trying to grab them directly and accidentally squishing them.
3. No glove, no swab
Okay, so this one’s not very catchy but it’s very important if you’re catching organisms for the purpose of studying their microbial ecosystem. We had to wear a new set of sterile gloves every time we caught a new subject, to prevent contamination from other samples and our own micro-biomes.
After catching our specimen, the first step was to rinse it with ultrapure water to wash out environmental debris such as algae or leaves. Then, we took care to use a sterile swab to take a microorganismal sample of three main zones: the mouth, skin and cloaca. This was often a cooperative effort, with one person securing the animal in place while the other sample the organisms that we were truly interested in: the invisible microbes.
All in all, our team had a great time getting a taste of the life of a field microbiome researcher. It’s clear that for someone who’s interested in analysing micro-biomes across different taxa within an ecosystem, you often need to get creative with your methods of collecting samples. And the field component is only a small part of the work! Back in the lab we learned how to dissect insects to sample their gut fauna, as well as techniques on how to extract DNA from our swabbed samples, sequence them and use reference databases to identify the diversity of bacterial taxa that call a host organism home. It was a fascinating process!
Okay, so I’m a primatologist NOT a collector of night-dwelling slimy creepy crawlies. So to put it mildly I was less than enthused to trudge through the dark swabbing lizards and putting bugs into Ziplock bags. Unless I am out searching for night monkeys (Aotus zonalis) I take no part in research endeavours between the hours of 9:00 pm to 6:00 am. I especially do not go out in the dark just to lunge down a steep flight of stairs bruising every natural surface on my body. However, even I must admit that our group’s night hike and subsequent research project was not without excitement. At the beginning of our night hike we ran into some researchers from Dr. Meg Crofoot’s lab who were tracking a male kinkajou as a part of the “Food for Thought” project. We were lucky enough to follow along and see this relatively reclusive animal up close. For me, this was especially interesting because I will be interning in Dr. Crofoot’s lab beginning February 5th, working on the very same project. For part of this project I will be collecting microbiome samples for Jordan Kueneman’s research from mammals that have been previously tagged, including the kinkajou we saw on the night hike.
The work currently being conducted on micro-biomes is opening the door for an entire frontier of science that has been relatively unexplored. The potential for new discoveries in this field is inevitable and extremely exciting. Micro-biomes play a role in the biological make-up of most species and studies are currently testing the ways in which they influence the behaviour and evolution of their hosts. Our study showed that micro-biomes varied between amphibian species on BCI, Panama. For example, we found that the toad species Atelopus certus was the most different in microbe composition when compared to the rest of our study species. Upon doing research we found that A. certus secretes a powerful toxin to protect itself from predators (Yotsu-Yamashita & Tateki, 2010). With this knowledge, future studies could be set up to explore the relationship between microbe composition and host biotoxins. The results of our research project showed that micro-biomes are species-specific and vary between species even when there is significant overlap in habitat. The questions we asked during our research project are questions that are broadly applicable to my future research in the field of primatology. Micro-biomes are unique in that they are influential in nearly all facets of biology. Whether you are interested in population genetics or ecology, there are likely research questions about micro-biomes that remain unanswered. For this reason, micro-biome research is pivotal to our understanding of biology and even I, a narrow-minded primatologist, have adopted an appreciation for microbes.
The opportunity to finally work with vertebrate’s micro-biomes was pretty exciting (after some very interesting talks on plant ecology I was itching for some animal stuff). So the night hike was pretty appealing to me. But I have to be honest, micro-biomes have been just a distant image in my scientific career. The first time I heard about the idea of micro-biomes in an ecological setting was during my masters program from a fellow grad student. He was studying how socialization in young green iguanas Iguana iguana (strict herbivores) could potentially change their gut micro-biomes, which are shown to be highly specialized in digesting plant material. He concluded that there was no significant exchange of gut micro-biomes among young iguanas. Our conversations brought us to talk about the Hoatzin Ophisthocomus hoazin, the only bird known to eat leaves (plant material) almost exclusively. This bird, unique in its kind, has incorporated a series of microbes into its gut that allows it to digest and process plant material that is otherwise very toxic to several species. After this few rare events “dealing” with micro-biomes my experience was limited to human digestive systems and other fads on what we should eat or what we shouldn’t.
The impact that micro-biomes could have on wild populations of a wide variety of species has never really occurred to me. Trying to understand and evaluate this potential effect was the main purpose of this module at BCI. Working with micro-biomes, as the name implies, means doing a lot of microbiology work and following protocols that are not common in other macro-ecology studies, such as the ones I have been used to. So the combination of hiking at night on a muddy river bank wearing rubber-boots (“gum-boots” for some rare specimens) looking for frogs or lizards and at the same time trying to take sterile samples of skin micro-biomes of the guys you catch, was pretty challenging. After a few tries I was an expert, catching only big and clumsy frogs (everything else would pretty much escape from me). But I guess now that micro-biomes of many organisms are not something they can escape easily from. Changes in micro-biomes of host organisms that have adapted to many specializations such as tree-frogs or other semi-aquatic reptiles may play a very important role in their fitness and overall survival. And considering that microbes are pretty sensitive (at least the “good guys”, not the disease causing ones), I think now that we should pay pretty close attention to what is happening not only in the macro-ecology scale, but also (quoting my classmate Gabriel Yahya Haage) in the “sweet, sweet micro-biomes” of many endangered (and why not all) species
Wehrle BA. 2013. Intergenerational lizard lounges do not explain variation in the gut microbiomes of green iguanas. Master’s Thesis. California State University, Northridge.
M. A. García-Amado, F. Michelangeli , P. Gueneau, M. E. Perez, M. G. Domínguez-Bello. 2007. Bacterial detoxification of saponins in the crop of the avian foregut fermenter Opisthocomus hoazin. J. Anim. Feed Sci. 16: 82–85
JG Kueneman, L Wegener Parfrey, DC Woodhams, HM Archer, RKnight and VJ. Mckenzie. 2014. The amphibian skin-associated microbiome across species, space and life history stages. Molecular Ecology 23, 1238–1250
Yotsu-Yamashita, M., & Tateki, E. 2010. First report on toxins in the Panamanian toads Atelopus limosus, A. glyphus and A. certus. Toxicon, 55(1), 153-156.